The 19-year-old Shaheen completed his four-wicket haul when he dismissed Rashid Khan, finishing with figures of 4-47 from 10 overs.
A sun-drenched day and baking hot temperatures made batting first in the day/night fixture an understandable decision.
"He chose the IPL and PSL, announced an early retirement and recused himself from the World Cup," said Akhtar in his video uploaded on Friday.
South Africa cannot now mathematically qualify for the semi-finals from the 10-team round-robin phase but Pakistan still have a slender chance of reaching the last four.
The India skipper admitted the offence and accepted the sanction proposed by match referee Chris Broad, the former England batsman.
New Zealand made a flying start to their World Cup campaign as paceman Matt Henry struck three times in a 10-wicket trashing of woeful Sri Lanka on Saturday.
David Warner hit an unbeaten half-century on his official return to international cricket on Saturday as Australia romped to victory by seven wickets in their World Cup opener against Afghanistan.
South Africa captain Faf du Plessis has challenged his side to make amends for the painful start to their World Cup campaign as they aim to bounce back against Bangladesh on Sunday.
The 24-year-old reached the milestone in his 68th innings during Pakistan's chase of a 238-run target. Babar took 11 innings more than South Africa's Hashim Amla, who reached the milestone in 57 innings, but overtook West Indies great Viv Richards (69 innings).
Mohammad Hafeez was the top scorer with a 62-ball 84 as Babar Azam (63 off 66) and captain Sarfraz Ahmed (55 of 44) also scored half centuries. England will need to pull off the highest successful run chase in World Cup history if they are to win this game.